Tandem mass spectrometry (MS/MS) is an established technique for improving the throughput of mass analysis in a mass spectrometer. Traditionally, one precursor is selected at a time, subjected to fragmentation and then its fragment analysed in the same or a subsequent mass analyser. When analysing complex mixtures (such as are typical for proteomics, environmental and food analysis), so many precursors must be analysed in a limited time period that there is insufficient time to achieve a good signal-to-noise ratio for each of the precursors. In consequence, tandem mass spectrometry techniques have been developed. Here, an incident ion beam is split into packets in accordance with their mass to charge ratio (m/z) and one packet is then fragmented without the loss of another packet, or in parallel with another packet.
The splitting of the ion beam into packets can be performed with a scanning device that stores ions of a broad mass range (such as a 3D ion trap: see for example WO-A-03/03010, or a linear trap with radial injection as for example in U.S. Pat. No. 7,157,698). Alternatively, ion beam splitting can be achieved through the use of a pulsed ion mobility spectrometer (eg as is disclosed in WO-A-00/70335 or U.S. Pat. No. 6,906,319), through a linear time-of-flight mass spectrometer as is shown in U.S. Pat. No. 5,206,508, or using multi-reflecting time-of-flight mass spectrometer (see, for example, WO-A-2004/008481). As yet another alternative, ion beam splitting can be achieved along a spatial coordinate as is disclosed for example in U.S. Pat. No. 7,041,968 and U.S. Pat. No. 7,947,950.
In each case, this first stage of mass analysis is followed by fast fragmentation, typically in a collision cell (preferably having an axial gradient) or by a pulsed laser. The resulting fragments are analysed (preferably by employing another TOF) on a much faster time scale than the scanning duration (so called “nested times”).
This approach provides throughput without compromising sensitivity. In a more traditional multi-channel MS/MS technique, by contrast, a number of parallel mass analysers (typically ion traps) are used to select one precursor each. The resultant fragments are then scanned out to an individual detector (e.g. the ion trap array shown in U.S. Pat. No. 5,206,506, or the multiple traps of U.S. Pat. No. 6,762,406). Other alternative arrangements, such as are shown in U.S. Pat. No. 6,586,727, U.S. Pat. No. 6,982,414, or U.S. Pat. No. 7,759,638, acquire all fragments from all precursors simultaneously, in one spectrum, which is then subsequently deconvoluted. However such traditional methods inherently lack dynamic range, and face challenges with reliability of identification.
The very limited time which is allocated for each fragment scan (typically, 10-20 microseconds) in the “nested times” approach of the above methods presents particular challenges. In particular, the “nested times” approach, involving the splitting of ion packets in time or space, inherently cannot provide high-performance analysis of obtained fragments. Increasing the scan time would further jeopardise the analytical performance of the precursor isolation, the latter already being quite poor when compared with routine present-day MS/MS. In addition, the “nested times” approach is incompatible with increasingly popular “slow” methods of fragmentation such as electron-transfer dissociation (ETD) which require up to a few tens of milliseconds for fragmentation to take place. Finally, the low transmission of the last-stage orthogonal-acceleration TOF offsets any advantages obtained by removal of losses in the precursor selection.